@inproceedings{2948,
  abstract     = {Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.},
  author       = {Tommasi, Tatiana and Quadrianto, Novi and Caputo, Barbara and Lampert, Christoph},
  location     = {Daejeon, Korea},
  pages        = {1 -- 15},
  publisher    = {Springer},
  title        = {{Beyond dataset bias: Multi-task unaligned shared knowledge transfer}},
  doi          = {10.1007/978-3-642-37331-2_1},
  volume       = {7724},
  year         = {2013},
}

@inproceedings{2973,
  abstract     = {Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building blocks of many practical cryptographic applications such as identification schemes, group signatures, and secure multiparty computation. Currently, first applications that critically rely on ZK-PoKs are being deployed in the real world. The most prominent example is Direct Anonymous Attestation (DAA), which was adopted by the Trusted Computing Group (TCG) and implemented as one of the functionalities of the cryptographic Trusted Platform Module (TPM) chip.

Implementing systems using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking, significantly more complex than standard crypto primitives, such as encryption and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming and error-prone, in particular for developers with minor or no cryptographic skills. 

In this paper we report on our ongoing and future research vision with the goal to bring ZK-PoK to practice by making them accessible to crypto and security engineers. To this end we are developing compilers and related tools that support and partially automate the design, implementation, verification and secure implementation of ZK-PoK protocols.},
  author       = {Bangerter, Endre and Barzan, Stefania and Stephan Krenn and Sadeghi, Ahmad-Reza and Schneider, Thomas and Tsay, Joe-Kai},
  editor       = {Christianson, Bruce and Malcolm, James A. and Matyas, Vashek and Roe, Michael},
  pages        = {51 -- 62},
  publisher    = {Springer},
  title        = {{Bringing Zero-Knowledge Proofs of Knowledge to Practice}},
  doi          = {10.1007/978-3-642-36213-2_9},
  volume       = {7028},
  year         = {2013},
}

@article{3116,
  abstract     = {Multithreaded programs coordinate their interaction through synchronization primitives like mutexes and semaphores, which are managed by an OS-provided resource manager. We propose algorithms for the automatic construction of code-aware resource managers for multithreaded embedded applications. Such managers use knowledge about the structure and resource usage (mutex and semaphore usage) of the threads to guarantee deadlock freedom and progress while managing resources in an efficient way. Our algorithms compute managers as winning strategies in certain infinite games, and produce a compact code description of these strategies. We have implemented the algorithms in the tool Cynthesis. Given a multithreaded program in C, the tool produces C code implementing a code-aware resource manager. We show in experiments that Cynthesis produces compact resource managers within a few minutes on a set of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business Media, LLC.},
  author       = {Chatterjee, Krishnendu and De Alfaro, Luca and Faella, Marco and Majumdar, Ritankar and Raman, Vishwanath},
  journal      = {Formal Methods in System Design},
  number       = {2},
  pages        = {142 -- 174},
  publisher    = {Springer},
  title        = {{Code aware resource management}},
  doi          = {10.1007/s10703-012-0170-4},
  volume       = {42},
  year         = {2013},
}

@article{3261,
  abstract     = {Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.},
  author       = {Dubuis, Julien and Tkacik, Gasper and Wieschaus, Eric and Gregor, Thomas and Bialek, William},
  journal      = {PNAS},
  number       = {41},
  pages        = {16301 -- 16308},
  publisher    = {National Academy of Sciences},
  title        = {{Positional information, in bits}},
  doi          = {10.1073/pnas.1315642110},
  volume       = {110},
  year         = {2013},
}

@article{331,
  abstract     = {We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents.},
  author       = {Li, Wenhua and Zamani, Reza and Rivera Gil, Pilar and Pelaz, Beatriz and Ibáñez, Maria and Cadavid, Doris and Shavel, Alexey and Alvarez Puebla, Ramon and Parak, Wolfgang and Arbiol, Jordi and Cabot, Andreu},
  journal      = {Journal of the American Chemical Society},
  number       = {19},
  pages        = {7098 -- 7101},
  publisher    = {ACS},
  title        = {{CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents}},
  doi          = {10.1021/ja401428e},
  volume       = {135},
  year         = {2013},
}

@misc{3321,
  author       = {Quadrianto, Novi and Lampert, Christoph},
  booktitle    = {Encyclopedia of Systems Biology},
  editor       = {Dubitzky, Werner and Wolkenhauer, Olaf and Cho, Kwang and Yokota, Hiroki},
  pages        = {1069 -- 1069},
  publisher    = {Springer},
  title        = {{Kernel based learning}},
  doi          = {10.1007/978-1-4419-9863-7_604},
  volume       = {3},
  year         = {2013},
}

@inproceedings{10749,
  abstract     = {Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures.},
  author       = {Polshyn, Hryhoriy and Budakian, Raffi and Gu, Genda},
  booktitle    = {APS March Meeting 2013},
  issn         = {0003-0503},
  location     = {Baltimore, MD, United States},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Cantilever micro-susceptometry of mesoscopic Bi2212 samples}},
  volume       = {58},
  year         = {2013},
}

@article{10895,
  abstract     = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. },
  author       = {Vanneste, Steffen and Friml, Jiří},
  issn         = {2223-7747},
  journal      = {Plants},
  keywords     = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics},
  number       = {4},
  pages        = {650--675},
  publisher    = {MDPI},
  title        = {{Calcium: The missing link in auxin action}},
  doi          = {10.3390/plants2040650},
  volume       = {2},
  year         = {2013},
}

@inproceedings{10897,
  abstract     = {Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.},
  author       = {Edelsbrunner, Herbert},
  booktitle    = {Graph-Based Representations in Pattern Recognition},
  isbn         = {9783642382208},
  issn         = {1611-3349},
  location     = {Vienna, Austria},
  pages        = {182--183},
  publisher    = {Springer Nature},
  title        = {{Persistent homology in image processing}},
  doi          = {10.1007/978-3-642-38221-5_19},
  volume       = {7877},
  year         = {2013},
}

@inproceedings{10898,
  abstract     = {A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered.},
  author       = {Haas, Andreas and Lippautz, Michael and Henzinger, Thomas A and Payer, Hannes and Sokolova, Ana and Kirsch, Christoph M. and Sezgin, Ali},
  booktitle    = {Proceedings of the ACM International Conference on Computing Frontiers - CF '13},
  isbn         = {978-145032053-5},
  location     = {Ischia, Italy},
  number       = {5},
  publisher    = {ACM Press},
  title        = {{Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation}},
  doi          = {10.1145/2482767.2482789},
  year         = {2013},
}

@inbook{10899,
  author       = {Barton, Nicholas H},
  booktitle    = {Encyclopedia of Biodiversity},
  isbn         = {978-0-12-384720-1},
  keywords     = {Adaptive landscape, Cline, Coalescent process, Gene flow, Hybrid zone, Local adaptation, Natural selection, Neutral theory, Population structure, Speciation},
  pages        = {508--515},
  publisher    = {Elsevier},
  title        = {{Differentiation}},
  doi          = {10.1016/b978-0-12-384719-5.00031-9},
  year         = {2013},
}

@inbook{10900,
  abstract     = {Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.},
  author       = {Weber, Michele and Sixt, Michael K},
  booktitle    = {Chemokines},
  editor       = {Cardona, Astrid and Ubogu, Eroboghene},
  isbn         = {9781627034258},
  issn         = {1940-6029},
  pages        = {215--226},
  publisher    = {Humana Press},
  title        = {{Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations}},
  doi          = {10.1007/978-1-62703-426-5_14},
  volume       = {1013},
  year         = {2013},
}

@inproceedings{10902,
  abstract     = {We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language.},
  author       = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Rubin, Sasha},
  booktitle    = {7th International Conference on Language and Automata Theory and Applications},
  isbn         = {9783642370632},
  issn         = {1611-3349},
  location     = {Bilbao, Spain},
  pages        = {214--225},
  publisher    = {Springer Nature},
  title        = {{How to travel between languages}},
  doi          = {10.1007/978-3-642-37064-9_20},
  volume       = {7810},
  year         = {2013},
}

@article{11083,
  abstract     = {Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML.},
  author       = {Franks, Tobias M. and HETZER, Martin W},
  issn         = {0962-8924},
  journal      = {Trends in Cell Biology},
  keywords     = {Cell Biology},
  number       = {3},
  pages        = {112--117},
  publisher    = {Elsevier},
  title        = {{The role of Nup98 in transcription regulation in healthy and diseased cells}},
  doi          = {10.1016/j.tcb.2012.10.013},
  volume       = {23},
  year         = {2013},
}

@article{11084,
  abstract     = {Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing.},
  author       = {Toyama, Brandon H. and HETZER, Martin W},
  issn         = {1471-0072},
  journal      = {Nature Reviews Molecular Cell Biology},
  keywords     = {Cell Biology, Molecular Biology},
  pages        = {55--61},
  publisher    = {Springer Nature},
  title        = {{Protein homeostasis: Live long, won't prosper}},
  doi          = {10.1038/nrm3496},
  volume       = {14},
  year         = {2013},
}

@article{11085,
  abstract     = {During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy.},
  author       = {Hatch, Emily M. and Fischer, Andrew H. and Deerinck, Thomas J. and HETZER, Martin W},
  issn         = {0092-8674},
  journal      = {Cell},
  keywords     = {General Biochemistry, Genetics and Molecular Biology},
  number       = {1},
  pages        = {47--60},
  publisher    = {Elsevier},
  title        = {{Catastrophic nuclear envelope collapse in cancer cell micronuclei}},
  doi          = {10.1016/j.cell.2013.06.007},
  volume       = {154},
  year         = {2013},
}

@article{11086,
  abstract     = {Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.},
  author       = {Liang, Yun and Franks, Tobias M. and Marchetto, Maria C. and Gage, Fred H. and HETZER, Martin W},
  issn         = {1553-7404},
  journal      = {PLoS Genetics},
  keywords     = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics},
  number       = {2},
  publisher    = {Public Library of Science},
  title        = {{Dynamic association of NUP98 with the human genome}},
  doi          = {10.1371/journal.pgen.1003308},
  volume       = {9},
  year         = {2013},
}

@article{11087,
  abstract     = {Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.},
  author       = {Toyama, Brandon H. and Savas, Jeffrey N. and Park, Sung Kyu and Harris, Michael S. and Ingolia, Nicholas T. and Yates, John R. and HETZER, Martin W},
  issn         = {0092-8674},
  journal      = {Cell},
  keywords     = {General Biochemistry, Genetics and Molecular Biology},
  number       = {5},
  pages        = {971--982},
  publisher    = {Elsevier},
  title        = {{Identification of long-lived proteins reveals exceptional stability of essential cellular structures}},
  doi          = {10.1016/j.cell.2013.07.037},
  volume       = {154},
  year         = {2013},
}

@article{11088,
  abstract     = {The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM.},
  author       = {Regner, Benjamin M. and Vučinić, Dejan and Domnisoru, Cristina and Bartol, Thomas M. and HETZER, Martin W and Tartakovsky, Daniel M. and Sejnowski, Terrence J.},
  issn         = {0006-3495},
  journal      = {Biophysical Journal},
  keywords     = {Biophysics},
  number       = {8},
  pages        = {1652--1660},
  publisher    = {Elsevier},
  title        = {{Anomalous diffusion of single particles in cytoplasm}},
  doi          = {10.1016/j.bpj.2013.01.049},
  volume       = {104},
  year         = {2013},
}

@article{115,
  abstract     = {We present the design and performance characterization of a new experimental technique for measuring individual particle charges in large ensembles of macroscopic grains. The measurement principle is qualitatively similar to that used in determining the elementary charge by Millikan in that it follows individual particle trajectories. However, by taking advantage of new technology we are able to work with macroscopic grains and achieve several orders of magnitude better resolution in charge to mass ratios. By observing freely falling grains accelerated in a horizontal electric field with a co-falling, high-speed video camera, we dramatically increase particle tracking time and measurement precision. Keeping the granular medium under vacuum, we eliminate air drag, leaving the electrostatic force as the primary source of particle accelerations in the co-moving frame. Because the technique is based on direct imaging, we can distinguish between different particle types during the experiment, opening up the possibility of studying charge transfer processes between different particle species. For the ∼300 μm diameter grains reported here, we achieve an average acceleration resolution of ∼0.008 m/s2, a force resolution of ∼500 pN, and a median charge resolution ∼6× 104 elementary charges per grain (corresponding to surface charge densities ∼1 elementary charges per μm2). The primary source of error is indeterminacy in the grain mass, but with higher resolution cameras and better optics this can be further improved. The high degree of resolution and the ability to visually identify particles of different species or sizes with direct imaging make this a powerful new tool to characterize charging processes in granular media.},
  author       = {Waitukaitis, Scott R and Jaeger, Heinrich},
  journal      = {Review of Scientific Instruments},
  number       = {2},
  publisher    = {AIP},
  title        = {{In situ granular charge measurement by free-fall videography}},
  doi          = {10.1063/1.4789496},
  volume       = {84},
  year         = {2013},
}